Basic and applied biological research and biotechnology are limited by our ability to get information into and out from living systems, and to act on information inside living systems. Endy (2005) Nature 438:449-53; Voigt (2006) Curr Opin Biotechnol 17:548-57; and Kobayashi et al. (2004) Proc Natl Acad Sci USA 101:8414-9. For example, there are only a small number of inducible promoter systems available to provide control over gene expression in response to exogenous molecules. Gossen et al. (1992) Proc Natl Acad Sci USA 89:5547-51; and Lutz et al. (1997) Nucleic Acids Res 25:1203-10. Many of the molecular inputs to these systems are not ideal for broad implementation, as they can be expensive and introduce undesired pleiotropic effects. In addition, broadly-applicable methods for getting information out of cells non-invasively have been limited to strategies that rely on protein and promoter fusions to fluorescent proteins, which enable researchers to monitor protein levels and localization and transcriptional outputs of networks, leaving a significant amount of the cellular information content currently inaccessible.
To address these challenges scalable platforms are needed for reporting on, responding to, and controlling any intracellular component in a living system. A striking example of a biological communication and control system is the class of RNA regulatory elements called riboswitches, comprised of distinct sensor and actuation (gene regulatory) functions, that control gene expression in response to specific ligand concentrations. Mandal et al. (2004) Nat Rev Mol Cell Biol 5:451-63. Building on these natural examples, engineered riboswitch elements have been developed for use as synthetic ligand-controlled gene regulatory systems. Kim et al. (2005) RNA 11:1667-77; An C I et al. (2006) RNA 12:710-6; Bayer et al. (2005) Nat Biotechnol 23:337-43; and Isaacs et al. (2006) Nat Biotechnol 24:545-54. However, as versatile as these early examples of riboswitch engineering are, there are additional challenges posed, such as greater ease in portability across organisms and systems, and improved modularity and component reuse.
There is a need, therefore, to develop a universal and extensible RNA-based platform that will provide a framework for the reliable design and construction of gene regulatory systems that can control the expression of specific target genes in response to various effector molecules.